Evolution

From Pulmogenomics.org

Biological evolution is the change in a population's inherited traits from generation to generation. These traits are encoded as genes that are copied and passed on to offspring during reproduction. Mutations and other random changes in these genes can produce new or altered traits, resulting in inheritable differences (genetic variation) between organisms. Evolution occurs when these differences become more common or rare in a population. This either happens through natural selection, which is caused by differences in the reproductive value of the traits, or randomly through genetic drift.

Natural selection occurs because organisms with traits that help them survive and reproduce tend to have more offspring. In doing so, they will pass more copies of their inheritable traits on to the next generation. This process causes advantageous traits to become more common over time, while disadvantageous ones become rarer.[1][2][3] Over many generations, this process can produce varied adaptations to environmental conditions.[4] As genetic differences in and between populations of a species accumulate, this species may split into new species. The similarities between organisms suggest that all known species are descended from a single ancestral species through this process of gradual divergence.[1][5][6]

The theory of evolution by natural selection was first put forth in detail in Charles Darwin's 1859 book On the Origin of Species. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the modern evolutionary synthesis.[4] With its enormous explanatory and predictive power, this theory has become the central organizing principle of modern biology, providing a unifying explanation for the diversity of life on Earth.[7][8][9]

History of evolutionary thought

Charles Darwin at age 51, just after publishing The Origin of Species.

Gregor Mendel's work on the inheritance of traits in pea plants laid the foundation for genetics.

Evolutionary ideas such as common descent and the transmutation of species have existed since at least the 6th century BCE, when they were expounded by the Greek philosopher Anaximander.[10] A variety of such ideas developed in the 18th century, and in 1809 Lamarck contended that transmutation of species occurred as parents passed on adaptations acquired during their lifetimes.[11] These ideas were seen in England as a threat to political and religious stability and strongly opposed by the scientific establishment.

In 1858 Charles Darwin and Alfred Russel Wallace jointly presented the theory of evolution by natural selection to the Linnean Society of London in separate papers.[12] This received little attention, but in 1859 the publication of Darwin's The Origin of Species provided detailed support for the theory and led to increasingly wide acceptance that evolution occurred. Darwin's specific ideas about evolution, such as gradualism and natural selection, were strongly contested at first. Lamarckists argued, for example, that waterfowl acquired webbed feet through their efforts to swim, rather than through a selective process of birds with some skin between their toes out-competing birds with none.[10] Eventually, when experiments failed to support it, this rival theory was abandoned in favor of Darwinism.

However, Darwin could not explain how traits were passed down from generation to generation or why variations in traits were not blended together through inheritance. A mechanism was provided in 1865 by Gregor Mendel, whose research revealed that distinct traits were inherited in a well-defined and predictable manner.[13] When Mendel's work was rediscovered in 1900, disagreements over the rate of evolution predicted by early geneticists and biometricians led to a rift between the Mendelian and Darwinian models of evolution. However, this contradiction was reconciled in the 1930s through the work of biologists such as Ronald Fisher. The end result was a combination of Darwinian natural selection with Mendelian inheritance, the modern evolutionary synthesis, or "Neo-Darwinism".[14] Finally, the identification of DNA as the genetic material by Oswald Avery in 1944,[15] and the subsequent publication of the structure of DNA by James Watson and Francis Crick in 1953,[16] demonstrated the physical basis for inheritance. Since then, genetics and molecular biology have become central to evolutionary biology.[17]

Heredity

A section of a model of a DNA molecule.[18] Also: animated version

For more details on this topic, see Introduction to genetics, Genetics, and Heredity.

Gregor Mendel's work on pea plants provided the first firm demonstration that heredity occurred in discrete units.[13] He was able to show that the traits were inherited from parent to offspring and that traits were discrete, since if one parent had round peas and the other wrinkled, the progeny were not intermediate, but either round or wrinkled. He also showed that the traits of the parents were distributed to progeny in a well-defined and predictable manner, which is now called Mendelian inheritance. His research laid the foundation for the concept of discrete heritable traits, known today as genes.[19] Mendel's ideas replaced the notion of "blending inheritance" prevalent at the time Darwin wrote The Origin of Species, and answered the long-standing problem of the persistence of variation within populations.

Later research gave a physical basis to the notion of genes, and eventually identified DNA as the heritable material, with genes re-defined as regions within this DNA.[19] DNA is stored within chromosomes in organisms and a specific location on a chromosome is known as a locus, with a variant of a DNA sequence at a given locus called an allele. DNA is not copied perfectly, and changes (mutations) in genes produce new alleles and thus affect the traits that the genes control. This simple correspondence between a gene and a trait works in many cases, although complex traits such as disease resistance are controlled by multiple interacting genes.[20][21]

Apart from mutations, other way changes in genes can influence traits is through DNA modifications such as DNA methylation, which do not change the sequence of the DNA in a gene, but cause an inherited change in the use of that gene.[22] Non-DNA based forms of heritable variation exist, such as transmission of the secondary structures of prions in yeast,[23] or structural inheritance of patterns in the rows of cilia in protozoans such as Paramecium[24] and Tetrahymena.[25] However, it is unclear if these mechanisms produce specific heritable changes in response to the environment. If this does occur, then some instances of evolution would be separate from standard genetic inheritance, which avoids any connection between the environment and the production of heritable variation.[26] However, the processes that produce these variations are rather rare and often reversible, so their significance to evolution remains unclear.[27]

Variation

For more details on this topic, see Genetic variation and Population genetics.

Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes during sexual reproduction (genetic recombination). In some organisms, like bacteria and plants, variation is also produced by the mixing of genetic material between different species in horizontal gene transfer and hybridization.[28][29] Despite all the processes that introduce variation, most sites in the genome of a species are identical in all individuals of this species.[30] However, relatively small changes in genotype can lead to dramatic changes in phenotype, with chimpanzees and humans, for example only differing in about 5% of their genomes.[31]

The heritable portion of an individual's traits, their phenotype, results from the interaction of their specific genetic makeup, or genotype with the environment.[21] Thus, the variation in heritable traits within a population reflects the variation in this population's genetic makeup. The modern evolutionary synthesis defines evolution as the change over time in the relative frequencies of alleles in a population.[32] The frequency of these variants may fluctuate in the population, becoming more or less prevalent relative to other alleles of that gene. All evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of fixation — when it either disappears from the population, or when it replaces the ancestral allele entirely.[33]

Mutation

For more details on this topic, see Mutation.

Mutation can occur because of "copy errors" during DNA replication

Genetic variation arises due to random mutations that occur in the genomes of all organisms. Mutations are transmissible changes in genetic material, and are often caused by mutagens such as radiation and mutagenic chemicals, as well as errors that occur during DNA replication.[34] Viruses and mobile DNA sequences such as transposons, are another cause of mutations.[35][36] In multicellular organisms, mutations can be classified into germline mutations that occur in the gametes and thus can be passed onto offspring, and somatic mutations that can cause the malfunction or death of cells and can also cause cancer.[34] Organisms have therefore evolved multiple mechanisms such as DNA repair that reduce mutation rates, although the optimal mutation rate for a species is a trade-off between costs such as the energy expended on DNA repair and the effects of deleterious mutations, and the benefits of advantageous mutations.[37] Organisms such as bacteria can even increase their mutation rate in response to stress, leading to the evolution of novel genes that counter the source of stress.[38]

Individual genes can be affected by two different types of mutations. In point mutations, a single base pair is altered. This change in a single base pair may or may not affect the function of the gene. The other type of mutations are the deletion and insertion of base pairs. These changes usually cause a loss of the gene's function, as they cause a shift in reading frame and thus change many amino acid codons simultaneously.[39]

Gene duplications, which may occur via a number of mechanisms, are believed to be one major source of raw material for evolving new genes, as tens to hundreds of genes are duplicated in animal genomes every million years.[40] Most genes belong to larger families of genes that are derived from one or more ancestral genes.[41] Novel genes can be produced either through duplication and divergence of an ancestral gene, or the recombination of protein domains to form a new combination of these structural modules.[42][43] The duplication of genomes to produce polyploid organisms also appears to have been important in evolution, particularly in plants.[44]

Large chromosomal rearrangements do not necessarily change gene function, but can result in reproductive isolation, and therefore cause speciation.[45] An example of chromosomal rearrangements is the fusion of two chromosomes in the Homo genus that produced human chromosome 2; this fusion did not occur in the chimpanzee lineage, and chimpanzees retain two separate chromosomes.[46] However, in this case, chromosomal rearrangements do not appear to have driven the divergence of the human and chimpanzee lineages.[47]

Recombination

For more details on this topic, see Genetic recombination.

In asexual organisms, variants in genes on the same chromosome will always be inherited together—they are linked, as they are joined together in the same DNA molecule. However, sexual organisms, can exchange DNA between two matching chromosomes in a process called genetic recombination.[48] This shuffling of genetic material between chromosomes allows even alleles of genes that are close together in the genome to be inherited independently. However, the recombination rate is not very high and in humans is approximately one recombination event per 1,000,000 base pairs.[49] Therefore, linked alleles are not always shuffled away from each other, but tend to be inherited together. This tendency is measured by comparing the co-occurrence of two alleles, their linkage disequilibrium. A set of alleles that are often inherited together is called a haplotype and this co-inheritance can indicate that the locus is under positive selection.[50]

Recombination in sexual organisms allows disadvantageous mutations to be purged and beneficial mutations to be retained more efficiently than in asexual organisms.[51] However, recombination can also lead to more individuals with new and advantageous gene combinations being produced. These benefits can be identified by looking at the effects of situations where alleles cannot be separated by recombination (for example in mammalian Y chromosomes).[52] In these situations, there is a reduction in effective population size called the Hill-Robertson effect,[53] which causes the accumulation of deleterious mutations.[54] These positive effects of recombination are balanced by the facts that it can cause mutations (as it involves the breaking and rejoining of the DNA strands) and it can also separate gene combinations that have been successful in previous generations.[51] The optimal rate of recombination for a species is therefore a trade-off between these conflicting factors.

Gene flow

For more details on this topic, see Gene flow, Hybrid, and Horizontal gene transfer.

Gene flow is the exchange of genes between populations, most commonly of the same species.[55] Examples include the migration of organisms and the exchange of pollen within a species, as well as hybridization and horizontal gene transfer between species.

Migration into or out of a population can change allele frequencies. Immigration may add new genetic material to the established gene pool of a population. Conversely, emigration may remove genetic material. As reproductive isolation is required for speciation, gene flow may delay speciation by homogenizing two diverging populations. Gene flow is hindered by impassable mountain ranges, oceans and deserts or even the Great Wall of China, which has hindered the flow of plant genes.[56]

Depending on how far two species have diverged since their last common ancestor, it may still be possible for them to produce viable offspring, as with horses and donkeys mating to produce mules.[57] Such hybrids are generally infertile, due to mispairings of chromosomes during meiosis. In this case, closely-related species may regularly interbreed, but hybrids will be selected against and the populations will remain distinct. This has been noted in toads, butterflies, clams and mussels. Selection against hybrids may produce traits that increase reluctance to mate outside the species and character displacement.[58] However, viable hybrids can also be formed and these new species can either have properties intermediate between their parent species, or a radically different phenotype.[59] Although hybridization rarely leads to new species in animals, this is an important means of speciation in plants.[44] Polyploidy, having more than two copies of each chromosome, is tolerated in plants more readily than in animals. The major advantage to a hybrid becoming polyploid is that it allows reproduction, as the different sets of chromosomes will be able to pair during meiosis.[60] Polypolids also have more genetic diversity, which allows them to resist the effects of inbreeding.[61]

Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring. Horizontal gene transfer is common among bacteria, even very distantly-related species.[62] In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can transfer them to many other species.[63] Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis may also have occurred.[64][65] Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.[66]

Horizontal gene transfer has also occurred within eukaryotes, from their chloroplast and mitochondrial genome to their nuclear genome.[67] According to endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell.[68] Horizontal gene transfer complicates phylogenetics, since it produces genetic connections between distantly-related species.[69]

Mechanisms of evolution

The two basic mechanisms of evolutionary change—the change in allele frequencies within a population—are genetic drift and natural selection. Genetic drift is the random sampling of a parent generation's genes, which causes some alleles to randomly change in frequency. Natural selection, on the other hand, is the nonrandom propagation of genes that favor survival and reproduction.

Genetic drift

For more details on this topic, see Genetic drift and Effective population size.

Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in the offspring generation are a random sample of alleles in the parent generation, and are thus subject to sampling error.[33] Over time, even in the absence of selection on the alleles, allele frequencies tend to "drift" upward or downward, until they eventually becoming "fixed" - that is, going to 0% or 100% frequency. Fluctuations in allele frequency between successive generations may thus result in some alleles disappearing from the population due to chance alone. Two separate populations that begin with the same allele frequencies might therefore drift apart by random fluctuation into two divergent populations with different sets of alleles.[70]

The relative importance of natural selection and genetic drift in determining the fate of new mutations depends on the population size and the strength of selection.[71] Natural selection is predominant in large populations, while genetic drift is dominant in small populations. Finally, the time for an allele to become fixed in the population by genetic drift (that is, for all individuals in the population to carry that allele) depends on population size — smaller populations require a shorter time for fixation.[72]

As a result, changing population size can dramatically influence the course of evolution. Population bottlenecks, where the population shrinks in size temporarily to a small number of individuals and therefore loses much genetic variation, result in a more uniform population and the loss of most rare variation.[33] Bottlenecks may also result from migration or population subdivision.[71]

Natural selection

For more details on this topic, see Natural selection.

A peacock's tail is the canonical example of sexual selection

Natural selection, one of the processes that drive evolution, results from the difference in reproductive success between individuals in a population.[73] It has often been called a "self-evident" mechanism because it necessarily follows from the following facts:

Natural, heritable variation exists within populations and among species

Organisms are superfecund (produce more offspring than can possibly survive)

Organisms in a population vary in their ability to survive and reproduce

In any generation, successful reproducers pass their heritable traits to the next generation, while unsuccessful reproducers do not.

If a trait increases the evolutionary fitness of the individuals that carry them, then those individuals will be more likely to survive and reproduce than other organisms in the population, thus passing more copies of this heritable trait on to the next generation. Conversely, a decrease in fitness caused by a deleterious trait results in this trait becoming rarer.[1][74][75]

A special case of natural selection is sexual selection: selection for any trait whose presence is directly correlated with mating success due to preferential mate choice.[76] Traits that evolved via sexual selection are particularly prominent among males of animal species. Despite the fact that such traits may decrease the survival of individual males (e.g. cumbersome antlers, mating calls or bright colors that attract predators, male-male fighting over access to mates),[77] reproductive success is usually higher in males that show robust, sexually selected phenotypes.[78]

Natural selection of trait frequencies within a population can be subcategorized into three different modes: directional selection (a shift in the mean trait value over time);[79] disruptive selection (selection for extreme trait values on both ends, or "tails" of the distribution, often resulting in a bimodal distribution and selection against the mean); and stabilizing selection (also called purifying selection — selection against extreme trait values on both ends, and a decrease in variance around the mean.)[80]

Outcomes of evolution

Adaptation

For more details on this topic, see Adaptation.

Through the process of natural selection, organisms generally become better suited to their environments.[73] As a result of increased fitness, natural selection can result in adaptation over time: the gradual accumulation of new traits that generally result in a population of organisms becoming better suited to its environment and ecological niche. Adaptation is often thought of as any evolutionary process that increases the fitness of the individual — however, under such a loose definition all natural selection would be considered adaptive. More strictly speaking, an adaptation is a specifically defined trait that not only enhances performance of some specific function, but also evolved under selection to perform that function (in other words, historical function must be the same as the current utility).[81]

It is important to note that not all characteristics of an organism are necessarily adaptations, as many traits are present in organisms simply by virtue of ancestry or developmental constraints. For example, whereas the human hand is very capable and seemingly well-adapted for operating a computer mouse, it is not an adaptation for that function since it did not evolve in a context where operating a mouse resulted in an increase of fitness. [4] Many traits that appear to be adaptations are in fact exaptations—traits that originally evolved under selection for one function, but were later co-opted for something else.[82] For example, the forelimbs of penguins were functionally wings before they evolved to function as aquatic flippers. [83] Additionally, adaptation has no objective or absolute value: a trait that increases fitness in one environment may decrease it in another. For example, light pigmentation is an advantageous adaptation for camouflage in light-colored habitats, but disadvantageous in dark-colored environments.[84]

Competition and cooperation

For more details on this topic, see Reciprocity (evolution) and Altruism in animals.

One of the most striking features of the natural world is that genes, cells, and organisms cooperate to make higher-order entities function. For example, cells in the human body do not generally grow uncontrollably as when they do, this causes cancer.[34] Generally, mathematical models incorporating mutation and natural selection have been used to model adaptation and evolution. Recent trends now incorporate "game theory" as more applicable to generating reliable models.[85][86] Cooperation is now seen as a fundamental property needed for evolution to construct new levels of organization. That selfish replicators could sacrifice their own reproductive potential to cooperate seems paradoxical in a competitive world, however a number of mechanisms can generate cooperation, such as kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection.[87] The ubiquity of cooperation in the natural world and studies from the last twenty-five years reveal cooperation as a significant principle in constructive evolution and it is now recognised as the third fundamental principle in evolution, alongside variation and selection.[88][89]

Speciation and extinction

For more details on this topic, see Speciation and Extinction.

The geographical isolation of Darwin's finches on the Galápagos Islands led to the rise of over a dozen distinct species. Their beak shapes reflect adaptations to many different food sources.

Speciation is the irreversible process by which a pre-existing species lineage diverges into two descendant (or "daughter") species lineages, which then become reproductively isolated.[90] Speciation is always described and understood as a binary (two-part) split in genealogy. Because a pair of sister species are equally descended from the ancestral form, it is incorrect to view one daughter species as the "original" species and the other as the "new" one.

In sexually reproducing organisms, speciation results from two important events: 1.) the evolution of reproductive isolating mechanisms, resulting in 2.) genealogical divergence. The most common mode of speciation in animals is allopatric speciation, which occurs in populations that initially become isolated geographically, such as by habitat fragmentation or migration. Simply by virtue of being geographically separated, selection and drift will act independently in the isolated populations, and will proceed to reproductive incompatibility if the separation is maintained long enough.[91] Sympatric speciation is species divergence without geographic isolation, and it is typically controversial since even a small amount of gene flow may be sufficient to homogenize a potentially diverging species.[92][93] General models of sympatric speciation require the evolution of stable polymorphisms associated with non-random assortative mating, in order for reproductive isolation to evolve. An example of rapid sympatric speciation can be clearly observed in the triangle of U, where new species of Brassica sp. have been made by the fusing of separate genomes from related plants, although this type of speciation may be more accurately described as speciation by polyploidization.

An Allosaurus skeleton. All non-avian dinosaur species died in a mass extinction.

Ernst Mayr's peripatric speciation is a type of speciation that exists as a result of character displacement on hybrid-zone boundaries between two adjoining populations. Peripatric speciation is a critical underpinning of the theory of punctuated equilibrium.

One common misconception about evolution is the idea that if humans evolved from monkeys, monkeys should no longer exist. However, biologists have never claimed that humans evolved from monkeys — only that humans and monkeys, like all organisms, share a common ancestor (that was neither human nor monkey).[94]Common misconceptions like this indicate a misunderstanding of speciation, which involves two subsets of a population cladogenetically splitting apart, rather than an entire species simply turning into a new one.

Extinction is the disappearance of species (i.e., gene pools). The moment of extinction is generally defined as occurring at the death of the last individual of that species. Extinction is not an unusual event on a geological time scale — species regularly appear through speciation, and disappear through extinction. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 90% of all marine species and 70% of all terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event, many forms of life perished (including approximately 50% of all genera), the most commonly mentioned among them being the non-avian dinosaurs. The Holocene extinction event is a current mass extinction, involving the rapid extinction of tens or hundreds of thousands of species each year. Scientists consider human activities to be the primary cause of the ongoing extinction event, as well as the related influence of climate change.[95]

Evidence of evolution

For more details on this topic, see Evidence of evolution and Common descent.

Common descent

The theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool. Evidence for common descent is inferred from traits shared between all living organisms. Today, there is strong evidence from genetics that all organisms have a common ancestor. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same 20 amino acids as the building blocks for proteins. The universality of these traits strongly suggests common ancestry, because the selection of many of these traits seems arbitrary. [96]

Morphologic similarities in the Hominidae family are evidence of common descent.

In the Origin of Species, Darwin built his case for the truth of shared ancestry of all organisms by pointing out a number of facts that were not new to science: 1.) organisms have geographic distributions that cannot be explained by local ecology or adaptation alone. 2.) The diversity of life is not a diversity of completely unique organisms, but a diversity of organisms that share traits and similarities with one another (see homology). 3.) Many organisms have vestigial traits or even behaviors that have no clear purpose in their modern bearers. 4.) All of life, as Linneaus and others have always recognized, can be naturally classified into a hierarchy of nested groups. This last point in particular is strongly consistent with a shared evolutionary history of all organisms that live today and ever lived.

Evolution has also left numerous signs of the histories of different species. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species.

The development of molecular genetics, and particularly of DNA sequencing, has allowed biologists to study the record of evolution left in organisms' genetic structures. The degrees of similarity and difference in the DNA sequences of modern species allows geneticists to reconstruct their lineages. It is from DNA sequence comparisons that figures such as the 96% genotypic similarity between humans and chimpanzees are obtained.[97][98]

Tiktaalik in context: one of many species that track the evolutionary development of fish fins into tetrapod limbs

Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, marsupials are found only in Australia and South America, showing that their common ancestor with placental mammals lived before the breakup of Gondwana and the freezing over of Antarctica.

Scientists correlate all of the above evidence, drawn from paleontology, anatomy, genetics, and geography, with other information about the history of Earth. For instance, paleoclimatology attests to periodic ice ages during which the world's climate was much cooler, and these are often found to match up with the spread of species which are better-equipped to deal with the cold, such as the woolly mammoth.

Morphological homology

Fossils are critical evidence for estimating when various lineages originated. Since fossilization of an organism is an uncommon occurrence, usually requiring hard parts (like teeth, bone, or pollen), the fossil record provides only sparse and intermittent information about ancestral lineages.[99]

The fossil record provides several types of data important to the study of evolution. First, the fossil record contains the earliest known examples of life itself, as well as the earliest occurrences of individual lineages. For example, the first complex animals date from the early Cambrian period, approximately 520 million years ago. Second, the records of individual species yield information regarding the patterns and rates of evolution, showing whether, for example, speciation occurs gradually and incrementally, or in relatively brief intervals of geologic time. Thirdly, the fossil record is a document of large-scale patterns and events in the history of life. For example, mass extinctions frequently resulted in the loss of entire groups of species, while leaving others relatively unscathed. Recently, molecular biologists have used the time since divergence of related lineages to calibrate the rate at which mutations accumulate, and at which the genomes of different lineages evolve.

Letter c in the picture indicates the undeveloped hind legs of a baleen whale, vestigial remnants of its terrestrial ancestors

Phylogenetics, the study of the ancestry of species, has revealed that structures with similar internal organization may perform divergent functions. Vertebrate limbs are a common example of such homologous structures. The bones within bat wings, for example, are very structurally similar to human hands due to common descent of these structures from an ancestor that also had 5 digits at the end of each forelimb. Other idiosyncratic anatomical features such as the panda's "thumb" indicate how an organism's evolutionary lineage constrains its adaptive development. Vestigial structures include the degenerate eyes of blind cave-dwelling fish, and the presence of hip bones in whales and snakes. Such structures may exist with little or no function in a more current organism, yet have a clear function in an ancestral species. Examples of vestigial structures in humans include wisdom teeth, the coccyx and the vermiform appendix.

These anatomical similarities in extant and fossil organisms can give evidence of the relationships between different groups of organisms. Important fossil evidence includes the connection of distinct classes of organisms by so-called "transitional" species, such as the Archaeopteryx, which provided early evidence for intermediate species between dinosaurs and birds,[100] and the recently-discovered Tiktaalik, which clarifies the development from fish to animals with four limbs.[101]

Molecular homology

By comparing the genetic and/or protein sequences of species, we can discern their evolutionary relationships. The resultant phylogenetic trees are typically congruent with traditional taxonomy, and are often used to either strengthen or correct taxonomic classifications. Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce. For example, neutral human DNA sequences are approximately 1.2% divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6% from gorillas, and 6.6% from baboons.[102][103] Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes.[104][105][106] The sequence of the 16S rRNA gene, a vital gene encoding a part of the ribosome, was used to find the broad phylogenetic relationships between all extant life. This analysis, originally done by Carl Woese, resulted in the three-domain system, arguing for two major splits in the early evolution of life. The first split led to modern bacteria, and the subsequent split led to modern archaea and eukaryotes.

Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged when new metabolic processes appeared, and it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor or by detecting their physical manifestations. For example, the appearance of oxygen in the earth's atmosphere is linked to the evolution of photosynthesis.

The proteomic evidence also supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase, are found in everything from the most primitive bacteria to the most complex mammals. The core part of the protein is conserved across all lineages of life, serving similar functions. Higher organisms have evolved additional protein subunits, largely affecting the regulation and protein-protein interaction of the core. Other overarching similarities between all lineages of extant organisms, such as DNA, RNA, amino acids, and the lipid bilayer, give support to the theory of common descent. The chirality of DNA, RNA, and amino acids is conserved across all known life. As there is no functional advantage to right- or left-handed molecular chirality, the simplest hypothesis is that the choice was made randomly by early organisms and passed on to all extant life through common descent. Further evidence for reconstructing ancestral lineages comes from junk DNA such as pseudogenes, "dead" genes which steadily accumulate mutations.[107]

There is also a large body of molecular evidence for a number of different mechanisms for large evolutionary changes, among them: genome and gene duplication, which facilitates rapid evolution by providing substantial quantities of genetic material under weak or no selective constraints; horizontal gene transfer, the process of transferring genetic material to another cell that is not an organism's offspring, allowing for species to acquire beneficial genes from each other; recombination, capable of reassorting large numbers of different alleles and of establishing reproductive isolation; and endosymbiosis, the incorporation of genetic material and biochemical composition of a separate species, a process observed in organisms such as the protist hatena and used to explain the origin of organelles such as mitochondria and plastids as the absorption of ancient prokaryotic cells into ancient eukaryotic ones.[108][109]

Evolutionary history of life

A phylogenetic tree of all extant organisms, based on 16S rRNA gene sequence data, showing the evolutionary history of the three domains of life, bacteria, archaea and eukaryotes. Originally proposed by Carl Woese

For more details on this topic, see Timeline of evolution.

Life must exist before it starts diversifying, and so the origin of life is a necessary precursor for biological evolution.[110] How life came to exist is not relevant to evolution,[111] and indeed Darwin wrote of "life, with its several powers, having been originally breathed by the Creator into a few forms or into one",[112] but the question of pre-evolutionary abiogenesis is a subject of scientific study[113] which is often discussed under the general heading of evolution.[110] The current scientific consensus is that life began from self-catalytic chemical reactions, but disputes over what defines life make the point at which such increasingly complex sets of reactions became true organisms unclear. Not much is yet known about the earliest developments in life. There is no scientific consensus regarding the relationship of the three domains of organisms (Archaea, Bacteria, and Eukaryota) or regarding the precise reactions involved in abiogenesis. Attempts to shed light on the origin of life generally focus on the behavior of macromolecules—particularly RNA—and the behavior of complex systems.

Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the 4.57 billion year history of Earth. Oxygenic photosynthesis emerged around 3 billion years ago, and the subsequent emergence of an oxygen-rich atmosphere made the development of aerobic cellular respiration possible around 2 billion years ago. In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the Cambrian explosion, a geologically brief period of remarkable biological diversity, originated all the major body plans, or phyla, of modern animals. This event may have been triggered by the development of the Hox genes.[114]

About 500 million years ago (mya), plants and fungi colonized the land, and were soon followed by arthropods and other animals. Amphibians first appeared around 300 mya, followed by reptiles, then mammals around 200 mya and birds around 100 mya. The human genus arose around 2 mya, while the earliest modern humans lived 200 thousand years ago.

Social and religious controversies

This caricature of Charles Darwin as an ape reflects the cultural backlash against evolution and common descent.

For more details on this topic, see Social effect of evolutionary theory, Creation-evolution controversy, and Objections to evolution.

Ever since the publication of The Origin of Species in 1859, evolution has been a source of controversy. In general, controversy has centered on the philosophical, social, and religious implications of evolution, not on the science of evolution itself; the proposition that biological evolution occurs through the mechanism of natural selection is completely uncontested within the scientific community.[115][116]

As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its applicability to human beings. Specifically, many object to the idea that all diversity in life, including human beings, arose through natural processes without a need for supernatural intervention. Although many religions, such as Catholicism, have reconciled their beliefs with evolution through theistic evolution, creationists object to evolution on the basis that it contradicts their theistic origin beliefs.[117] In some countries — notably the United States — these tensions between scientific and religious teachings have fueled the ongoing creation-evolution controversy, a social and religious conflict especially centering on politics and public education. While other fields of science, such as cosmology[118] and earth science,[119] also conflict with literal interpretations of many religious texts, evolutionary biology has borne the brunt of these debates.

Evolution has been used to support philosophical and ethical views which most contemporary scientists consider to have been neither mandated by evolution nor supported by science.[120] For example, the eugenic ideas of Francis Galton were developed into arguments that the human gene pool should be improved by selective breeding policies, including incentives for reproduction for those of "good stock" and disincentives, such as compulsory sterilization, "euthanasia", and later, prenatal testing, birth control, and genetic engineering, for those of "bad stock". Another example of an extension of evolutionary theory that is now widely regarded as unwarranted is "Social Darwinism", a term given to the 19th century Whig Malthusian theory developed by Herbert Spencer into ideas about "survival of the fittest" in commerce and human societies as a whole, and by others into claims that social inequality, racism, and imperialism were justified.[121]

^ Wallace A and Darwin C., "On the Tendency of Species to form Varieties, and on the Perpetuation of Varieties and Species by Natural Means of Selection," Jour. of the Proc. of the Linnean Society (Zoology), 3 (July 1858): 53-62

^ abDarwin, Charles (1872), The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life., London: John Murray 6th edition; with additions and corrections. Retrieved on 2006-12-31

^Leakey, Richard; Lewin, Roger (1996). The Sixth Extinction : Patterns of Life and the Future of Humankind. Anchor. ISBN 0-385-46809-1.

^ "Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species cannot be done conclusively by determining evolutionary trees for single genes." See Melcher, M (2001). Horizontal Gene Transfer. Oklahoma State University. Retrieved on 2007-04-18.

^Chen, FC; Li, WH (2001). "Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees". American Journal of Human Genetics68: 444-56. Retrieved on 2007-03-16.

^ The picture labeled "Human Chromosome 2 and its analogs in the apes" in the article Williams, Robert. Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry. Retrieved on 2007-03-17. shows how humans have a single chromosome which is two separate chromosomes in the nonhuman apes.

^Voight, BF; Kudaravalli, S; Wen, X; and Pritchard, JK (2006). "A Map of Recent Positive Selection in the Human Genome". PLoS Biol4 (3). DOI:10.1371/journal.pbio.0040072. Retrieved on 2007-03-17., states the International HapMap Project is "providing the strongest evidence yet that humans are still evolving" and details some of that evidence.

^ An overview of the philosophical, religious, and cosmological controversies by a philosopher who strongly supports evolution is: Dennett, D (1995). Darwin's Dangerous Idea: Evolution and the Meanings of Life. Simon & Schuster. ISBN 978-0684824710.

^ For more information on the scientific and social reception of evolution in the 19th and early 20th centuries, see: Bowler, PJ (2003). Evolution: The History of an Idea, Third Edition, Completely Revised and Expanded. University of California Press. ISBN 978-0520236936.

^ Darwin strongly disagreed with attempts by Herbert Spencer and other to extrapolate evolutionary ideas to all possible subject matters; see Midgley, M (2004). The Myths we Live By. Routledge, 62. ISBN 978-0415340779.

^ On the history of eugenics and evolution, see Kevles, D (1998). In the Name of Eugenics: Genetics and the Uses of Human Heredity. Harvard University Press. ISBN 978-0674445574.